Chunk #24 — Materials and Methods — Using pedigree information to improve phase, infer recombination events and detect genotyping error — Duo HMM

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A general approach for haplotype phasing across the full spectrum of relatedness.

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To carry out this inference we have developed an HMM that allows for SEs in the parental and child haplotypes. We use and to denote the probability of a SE on the parental or child haplotypes between two adjacent markers respectively. We also use to denote the probability of a recombination occurring between markers and . Specifically we use where is the genetic distance between markers and . We use the genetic distances from the HapMap LD based map [35] (which are inherently sex averaged) and scale them to the sex-specific genetic lengths from the deCODE 2002 map according to the sex of the parent.